AnnotationPipeline step -- from preliminary sqlite to sanctionedSqlite for a single organism

gistfile1.txt

# This function can be run in a 'newPkgs' folder after sufficient
# results have been obtained in annosrc/db, to produce a sanctionedSqlite database
# for a single organism

# the following constants are crucial

whattype <- tolower("OrgDb")
wheretoput <- 20250301 
theversion <- "3.21.0"
dbBaseDir <- "/home/rstudio/BSAnnoPipe/CODE/BioconductorAnnotationPipeline/annosrc/db/"
outDir <- "sanctionedSqlite"
if (!file.exists(outDir))
        dir.create(outDir)

# verify 'wheretoput' is numeric -- not a great validation

if(isTRUE(is.nan(as.numeric(wheretoput))))
    stop(paste("The second argument was", wheretoput, "but should instead be something like 20200910"),
         call. = FALSE)

# verify 'theversion' syntax

if(length(grep("^[0-9]+\\.[0-9]+\\.[0-9]+$", theversion)) != 1L)
    stop(paste("The third argument was",theversion,"but should instead be something like 3.11.0"),
         call. = FALSE)

# these must succeed, the R-libraries is otiose and should be eliminated

.libPaths(c("~/R-libraries", .libPaths()))
library(AnnotationForge)
library(AnnotationDbi)

metaDataSrc <- paste0(dbBaseDir, "metadatasrc.sqlite")

# supply values below
              
whatiamdoing = # something like "FLY_DB" -- is there validation?
chipsrc_name = # something like "chipsrc_fly.sqlite" -- check existence?
prefix = # something like org.Dm.eg and the mapping to 2-letter token should be formalized

cat(sprintf("building %s\n", whatiamdoing))

# how do we check the result of this call to verify or explain adverse events?

populateDB( whatiamdoing, prefix = prefix,
  chipSrc = paste0(dbBaseDir, chipsrc_name),
  metaDataSrc = metaDataSrc,
  outputDir = outDir)